Virology Lecture Note
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  • 1. VIROLOGY MIC 303; C; 2.0 VIRAL TAXONOMY ANJORIN, A. A., Virology & Immunology Research Group, Department of Microbiology, Lagos State University, Ojo
  • 2. OUTLINE  Introduction and Objectives  Definitions  Principles of Viral Taxonomy  Rules  Criteria for Viral Classification  Viral families  Family of Subviral Agent  Classical Examples  Summary  Further studies
  • 3.  Our elementary understanding  Interactive session  At the end of our discussion, we should all be able to: 1. 2. 3. INTRODUCTION AND OBJECTIVES
  • 4. DEFINITIONS IN VIRAL TAXONOMY  The word Viral is from Virus Obligate intracellular entity  The word taxonomy –A Science with dynamic field, based on information  Uses techniques and theories of: -Collating and describing; identification and classification; grouping and naming of viruses  But Nomenclature is just naming  Acronym ICNV ICTV  Virology, > 100yrs; Viral taxon (ICNV, 1960; ICTV, 1966 )
  • 5.  Systematics is the science of organizing the history of the evolutionary relationships of organisms.  Classification is determining the evolutionary relationships between organisms.  Identification is recognizing the place of an organism in an existing classification scheme, often using dichotomous keys to identify the organism.  Taxonomy (nomenclature) is assigning scientific names according to agreed international scientific rules.  The official taxonomic groups (from the largest to the smallest are):  Kingdom (e.g., animals, plants, bacteria; does not apply to viruses)  Phylum (e.g., vertebrates; does not apply to viruses)  Class (group of related orders; does not apply to viruses)  Order (group of related families)  Family (group of related genera)  Genus (group of related species)  Species, the smallest taxonomic group
  • 6. ICTV. http://talk.ictvonline.org  Formed and governed by the Virology Division of the International Union of Microbiological Societies (IUMS)  ICTV is composed of member Executive Committee (world experts on viruses) supported by numerous subcommittees and study groups  Operates an authoritative database (ICTVdB) containing taxonomic information  Presents report to International Congress of Virology  Update publication on taxonomy at approximately 3- year intervals
  • 7. Objectives  ICTV official objectives are to:  develop an internationally agreed taxonomy for viruses  develop internationally agreed names for taxa, including species and subviral agents  communicate decisions to all users particularly the international community of virologists  maintain an index of virus names  maintain an ICTV database, that records the data that characterize each named viral taxon, with their common names in all major languages
  • 8. Principles  ICTV essential principles of virus nomenclature are:  Stability  Rejection (prevents confusing names)  Necessity (avoids unnecessary name creation)
  • 9. ICTV 2011Official taxonomy  ICTV Classification system is Non systematic based upon the opinionated usage of data  Estimated 400,000 different viruses virologist believe may exist  Today > 5,000 viruses have been identified.  Number of recognized hierarchical taxa include:  6 Order  94 families ( > 24 families cause disease in human)  22 Sub families  395 Genera  2,480 Species
  • 10. The Order taxonomy  Classification of the 6 orders include:  Order: Caudovirales(3 Families)  Order: Herpesvirales(3 Families)  Order: Mononegavirales(4 Families)  Order: Nidovirales(3 Families)  Order: Picornavirales(5 Families)  Order: Tymovirales(4 Families)  72 Virus families are yet to be assigned to order
  • 11. Viral Taxonomy Methods  A monothetic system of classification is defined as a system based on a single characteristic or a series of single characteristics.  Polythetic is defined as sharing a number of common characteristics, without any one of these characters being essential for membership
  • 12.  System that is currently being used is a -Non systematic, polythetic, hierarchical system. -Differs from any other system in use for other organisms but it is effective, useful, and has withstood the test of time  Using the polythetic approach, a given virus grouping is defined by a collection of properties rather than a single property -and virus groups in different branches of the taxonomy can be characterized by different collections of properties
  • 13. BASIC TERMS IN VIRAL TAXONOMY  VIRION Entire infectious viral particle in nature  VIROID - They are the smallest known plant pathogens - They consist of a circular, single-stranded RNA that does not encode a protein (Cho et al., 2013) - the smallest known infectious agents. They are much smaller than the smallest genomes of viruses and have no genes for encoding proteins. After invading a host cell, viroids are thought to mimic the cell's DNA, so that the cell's RNA polymerase replicates them in the nucleus. Viroids are believed to cause disease by interfering with the host cell's gene regulation. They are destructive to many important commercial plants, including potatoes, tomatoes, cucumbers, coconuts, and chrysanthemums.
  • 14.  VIRUSOIDS -SSRNA satellite viruses; larger RNA to viroid -Consist of a single-stranded RNA genome encapsidated in stolen capsid of helper virus i.e. No gene to code for their own structural protein  the smallest of viruses; a plant virus with its RNA arranged in a circular chromosome without a protein coat. A virusoid is an infectious agent that infects plants in conjunction with an assistant virus; the assistant virus harbours the virusoid and is required for successful infection. Virusoids, while being studied in virology, are not considered as viruses but as subviral particles. Since they depend on helper viruses, they are classified as satellites.
  • 15.  VIRINO -Proteinacious infectious particle i.e. Possess Capsid + NA together in Association -N.A. (About 10-12nm) -Also Non Immunogenic
  • 16.  VIROPLASM -A.k.a factory site/ site for assembly of sub viral particles -Modified region where active viral replication takes place in a viral infected cell  SATELLITE VIRUS -A defective virus -Depends on helper virus for its replication.  DEFECTIVE VIRUS - A virus which is unable to replicate because it lacks a complete genome
  • 17. VIRAL TAXONOMICAL RULES  Nomenclature and Classification of viruses do not Use Conventional Taxonomic Groups  Suffix ending: -Viral family -Sub family -Order -Genus
  • 18.  The nucleic acid of DNA viruses is usually double stranded(ds) linear or circular molecules with the exception of parvovirus which has single stranded(ss) DNA.  The nucleic acid of RNA viruses is usually single stranded(ss) with the exception of the reoviruses (dsRNA)  In Sense (positive/plus strand viruses), the genome has the same polarity as the viral mRNA and thus can function as mRNA.  In Antisense (negative/minus strand viruses), the genome has the polarity opposite to that of the mRNA and therefore cannot be translated into proteins until it has first been transcribed into a complementary strand
  • 19. Rules for Taxa  Species  A species name shall consist of as few words as practicable but must not consist only of a host name and the word virus.  A species name must provide an appropriately unambiguous identification of the species.  Numbers, letters, or combinations thereof may be used as species where such numbers and letters are already widely used.  Newly designated serial numbers, letters or combinations thereof are not acceptable alone as species epithets. If a number or letter series is in existence it may be continued.
  • 20.  Genera  A virus genus is a group of related species that share some significant properties and often only differ in host range and virulence.  A genus name must be a single word ending in virus.  Approval of a new genus must be accompanied by the approval of a type species.
  • 21.  Subfamilies  A subfamily is a group of genera sharing certain common characters.  Taxon shall be used only when it is needed to solve a complex hierarchical problem.  A subfamily name must be a single word ending in virinae.
  • 22.  Families  A family is a group of genera, whether or not these are organized into subfamilies, sharing certain common characters.  A family name must be a single word ending in viridae.
  • 23.  Orders  An order is a group of families sharing certain common characters.  An order name must be a single word ending in virales.
  • 24. CRITERIA FOR VIRAL CLASSIFICATION  N. A. type 1. DNA 2. RNA viruses
  • 25. Nature and Strandedness Nature can be: Linear/ Circular Segmented/ Non segmented genome or Based on Polarity. Polarity I. Sense strand (positive/plus strand) II. Antisense strand
  • 26. I. Sense strand (Positive/plus strand)  The genome has the same polarity as the viral mRNA and thus can function as mRNA  A ssRNA+ means a genome with full, correct information, in the right position and can act as a template for translation
  • 27. II. Antisense strand (Negative/minus strand)  The genome has the polarity opposite to that of the mRNA and therefore cannot be translated into proteins until it has first been transcribed into a complementary strand
  • 28. Strandedness can be Single-stranded (ss) or double-stranded (ds) Baltimore’s work:  ss RNA + ve  ds RNA-/ + ( - means Abnormal/ + because it is double stranded)  ss DNA – ( - means Abnormal because DNA should be doubled)  ds DNA +/ -  There is another ss RNA + ve for Retro viruses called (ss Retro RNA +)  And there is also ss RNA that is negative known as (ss RNA –ve) (Abnormal )
  • 29. Classification of Viruses based on Genomic composition and their Pathway of mRNA formation
  • 30. Enzyme possession  Reverse transcriptase  Haemagglutinin enzyme (H) contained in the spike and is required for adsorption and penetration of Orthomyxo viruses into the host cells.  Neuraminidase enzyme (N) contained in another type of spike and it is required for invasion and release of influenza viruses  Polymerase enzymes -RNA-dependent RNA polymerase in RNA viruses -DNA polymerase in smallpox virus -RNA-dependent DNA polymerase (Reverse transcriptase) in hepatitis B viruses and retroviruses
  • 31. Enzyme Components
  • 32. Size and Morphology -Size include:
  • 33. -Morphology
  • 34. Susceptibility to Physical and Chemical Agents  Heat (50- 60o C; 30 min. death) and Cold (+4, -20, -60, - 80, -196 LN, -252 LH)  Room temperature +15 to +30  Refrigeration +2 to +8  Frozen -5 to -25  Ultra -68 to -85  LN-190  Virucidals: Hypochlorite, Isopropanol, Ether, O.As (H2O2)  Chemotherapeuticals -Not antibiotic (Viral purification) -Nucleotide Analogues- Polyomavirus -Nucleoside Analogues- HIV, Lassa
  • 35. Mode of transmission 1. Respiratory route viruses  Influenza  Measles viruses, e.t.c. 2. Transovarian (infected sperm to embryo) route viruses e.g.  Cytomegalovirus  HIV-1, e.t.c.
  • 36. Host, tissue and Cell tropism
  • 37. Immunological properties 1. Immunogenic 2. Non- Immunogenic viruses e.g.  Subvirals, etc
  • 38. Pathology 1. Inclusion body formation 2. CPE on Cells e.g. on  Hela cell, HEP 2, etc 3. Multinucleated Giant Cell producing viruses
  • 39. Symptomatology 1. Koplik spot viruses 2. Haemorrhagic Viruses e.g.  Rift valley  CHIK  DENG 3. Skin Jaundice 4. Salivation
  • 40. Place of first Isolation  Africa, Asia, etc  First isolated in Nigeria  Mokola (Hill, 1970)  Kotonkanvirus  Potiskumvirus  Yabapox (NIMER)  Igbo-Oravirus
  • 41.  Dugbevirus  Nairovirus (Nigeria in 1967)  Ileshavirus  Lassa virus (NE, 1969)  Lagos bat virus (LBV)(Eidolon helvum, 1956, Island)
  • 42. Organism of Natural host  Ranapox  Chordopox  Monkeypox  Bufallopox
  • 43. Sigla formation Method  Yatapox (Tanapox, Japan)  Hepadna  Papova  Picorna  Reo  Birna
  • 44. After the Researcher who discovered it  Epstein-Barr virus
  • 45. Presence or Absence of Envelope  Naked  Enveloped viruses
  • 46. Taxonomy of Viral Families A. DNA Viruses Adenoviridae (Greek Adenos- Gland) 1. Genus Mastadenovirus 2. Genus Aviadenovirus  Adenoviruses 1-49  Human Adenoviruses
  • 47. Baculoviridae (Latin Baculum-Rod-like) Virus infects invertebrates Genus Nucleopolyhedrovirus Genus Granulovirus
  • 48. Hepadnaviridae (Sigla, Hepatic- Liver) Hepatitis B Virus
  • 49. Herpesviridae (Greek Herpes- Creeping) 1. Subfamily Alphaherpesvirinae, Genera : Simplexvirus, Varicellovirus 2. Subfamily Betaherpesvirinae, Genera : Cytomegalovirus, Muromegalovirus, Roseolovirus 3. Subfamily Gammaherpesvirinae, Genera : Lymphocryptovirus, Rhadinovirus Unclassified viruses: 48 known. Genus Human Herpes Virus (HHV): HHV- 1 (Herpes Simplex Virus 1) HHV- 2 (Herpes Simplex Virus 2) HHV- 3 (Varicella Zoster Virus) HHV- 4 (Epstein- Barr Virus) HHV- 5 (Cytomegalovirus) HHV- 6 (Herpes Lymphotropic Virus) HHV- 7 (Human Herpes Virus 7) HHV- 8 (Kaposi)
  • 50. Iridoviridae (Word Iridescent, Many bright colour, Changes in light). Four Genera:  Iridovirus (Arthropods, type species: Invertebrate iridescent virus 6)  Chloriridovirus ( Also, Insects)  Ranavirus  Lymphocystivirus (fish)
  • 51. Papovaviridae (Sigla, Old and discontinued family, Now divided)
  • 52. Papillomaviridae (Warts and Condylomas- M. Membrane) Sixteen Genera: HPV Bovine PV, etc
  • 53. Parvoviridae (Greek Parvus- Small) 2 subfamilies: I. Parvovirinae (Five Genera):  Parvoviruses (Animal, Canine Parvoviruses)  Erythroviruses (B19)  Dependoviruses  Amdoviruses  Betaparvoviruses II. Densovirinae Invertebrates
  • 54. Plasmaviridae (Greek Plasma- Shaped product)  Mycoplasma
  • 55. Poxviridae (Greek Poc/ Pocc- Pustule) Subfamily Chondropoxvirinae Subfamily Entomopoxvirinae Unclassified viruses Smallpox Virus Vaccinia Virus Monkeypox and Bufallopox Molluscum Contagiosum Virus
  • 56. Polyomaviridae (Greek Poly- many, oma- Cancer)  BK Virus (BKV)  JC Virus (JCV)  Simian Virus (Monkey)  Bovine polyoma virus  Mouse polyoma virus  Rat polyoma virus, etc
  • 57. Others DNA Viruses  Ds non enveloped  Caulimoviridae  Myoviridae  Phycodnaviridae  Tectiviridae  Ss non enveloped  Circoviridae
  • 58. B. RNA VIRUSES Arenaviridae (Latin: Arenosus- Sandy) Genus Arenavirus A. Subgroup Tacaribe Complex (New world arenaviruses) Lymphocytic Choriomeningitis V. B. Subgroup LCM-LASV Complex (Old world arenaviruses)  Lassa Fever Virus  Sabia Virus  Guanarito Virus  Machupo Virus
  • 59. Astroviridae (Greek Astron- Star-like) Genus Astrovirus Human Astroviruses
  • 60. Birnaviridae (Sigla, Bi-Double Stranded genome). Three Genera affecting fish, chickens and insects:  Aquabirnavirus  Avibirnavirus  Entomobirnavirus
  • 61. Bornaviridae  Genus Bornavirus  Borna Disease Virus
  • 62. Bunyaviridae (Bunyamwera, Uganda) Seven groups (19 viruses) and 22 ungrouped viruses: Genus Bunyavirus e.g. Bunyamwera, La Cross virus Genus Hantavirus e.g. Hantaan Genus Phlebovirus e.g. Rift VFV Genus Nairovirus e.g. Crimean- Congo Haemorrhagic Fever Virus
  • 63. Caliciviridae (Greek Calix- Cup) Hepatitis E Virus (Provisional) Human Caliciviruses
  • 64. Coronaviridae (Greek Corona- Crown/ Petal- like) Genus Torovirus Genus Coronavirus e.g. Human Coronavirus- SARS Virus
  • 65. Cystoviridae ds positive non segmented enveloped Genus Cystovirus e.g. Pseudomonas syringae phage phi6
  • 66. Filoviridae (Greek Filo- Thread-like) Order Mononegavirales Genus Filovirus Ebola Virus (Ebola river in Zaire, 1976) Marburg Virus (1st, Lab Workers in Europe, 1967)
  • 67. A. BSL4 B. KITTING
  • 68. Flaviviridae (Greek Flavus- Yellow) 1. Pestivirus (Bovine Diarrhoae virus) 2. Hepatitis C-like viruses (Hepatitis C and G Viruses) 3. Genus Flavivirus Yellow Fever V. (Aedes aegypti). 2 types: Urban &Jungle Dengue Virus West Nile Virus (Uganda West Nile District ) Potiskum Virus (Mice, 1969) Zika Virus (Uganda Zika forest Monkey, 1947, Also Nigeria)
  • 69. Orthomyxoviridae (Greek Ortho-Straight, Myxo- Mucous) Surface projections of envelope distinct; About 500 spikes 8 gene segments (PB1, PB2, PA, HA, NP, NA, M, NS). -Epidemics and pandemics by Antigenic Drift (accumulation of point mutations=Gradual changes) and Shift (major antigenic changes=new subtype into human population). 1. Genus Influenzavirus A 2. Genus Influenzavirus B 3. Genus Influenzavirus C 4. Genus Thogoto-like Viruses
  • 70. Paramyxoviridae (Greek Para- By the side of; Myxo-) Two Subfamilies: 1. Pneumovirinae Respiratory Syncytial Virus 2. Paramyxovirinae Genus Paramyxovirus e.g. Human paramyxovirus and H parainfluenza 1
  • 71. Contd.: Paramyxoviridae Genus Morbilivirus e.g. Measles Virus Genus Rubulavirus e.g. Mumps Virus
  • 72. Picornaviridae (Sigla, Greek Pico- Small) 1. Genus Enterovirus e.g. Enteroviruses 68, 70, 71 Polio Virus and Coxsackie 2. Genus Rhinovirus Human rhinovirus 1A 3. Genus Hepatovirus  Human hepatitis A virus 4. Genus Cardiovirus Encephalomyocarditis virus 5. Genus Aphthovirus Foot and Mouth Disease V.
  • 73. Reoviridae (Sigla, R.E.O. ). Four Genera- Medicals. Genus Orthoreovirus- Human Reovirus Genus Rotavirus- Human rota Genus Coltivirus- Colorado Tick fever Virus Genus Orbivirus-Orungo V. Others Aquareovirus Cypovirus e.g. Cypovirus type 1-12 Fijivirus, etc
  • 74. Genus Rotavirus  There are five species of : A, B, C, D, and E  3 Human rotaviruses: A, B and C  Rotavirus A: Different strains called serotypes  6 structural (viral) proteins: VP1, VP2, VP3, VP4, VP6 and VP7  6 NSPs only produced in cells infected by rotavirus: NSP1, NSP2, NSP3, NSP4, NSP5 and NSP6  2 genes determine G-types and P-types of A  Glycoprotein VP7 defines the G serotypes (G1- 6,891012) and protease- sensitive protein VP4 defines P serotypes (P1, 4, 6, 8-11)
  • 75. Retroviridae (Sigla, Reverse transcriptase) Subfamilies: Oncovirinae, Lentivirinae, Spumavirinae Seven Genera 1. Genus Gammaretroviruses 2. Genus Episilonretroviruses 3. Genus Alpharetroviruses 4. Genus Betaretrovirus group 5. Genus Deltaretroviruses 6. Genus Lentivirus e.g. HIV Human T- Leukaemia Virus Type 1 and 2 7. Genus Spumavirus
  • 76. Rhabdoviridae (Greek Rhabdo-Straight bullet- shaped) Genus Vesiculovirus e.g. Rhabdovirus Genus Lyssavirus e.g. Rabies Virus Mokola Virus Genus Ephemerovirus Others
  • 77. Togaviridae (Latin Toga- Mantle or Cloak, A Cover/ layer) because the virions are surrounded by a lipid envelope and haemagglutinin spikes 1. Genus Alphavirus SFV Chikungunya Virus Igbo-Ora Virus; Sindbis virus 2. Genus Rubivirus Rubella (from latin word- little red) Virus (German measles) Only virus of the Genus
  • 78. Toroviridae (Latin Torus- Lowest Convex)  Some consider Torovirus as a Genus in the family Coronaviridae  Human toroviruses
  • 79. Others RNA Viruses  Non enveloped  Potyviridae
  • 80. TAXONOMY OF SUBVIRAL AGENTS -Taxonomical Properties of subviral agents include: i. No Genome ii. No I.R. iii. Filterable size iv. No inactivation by heat, disinfectant and UV light v. Tend to be modified human protein that is infectious vi. Usually tend to form insoluble aggregate of fibrils vii. Only Clinical diag. but just one Lab. Diag.: Histology of Brain
  • 81. Rules in Naming sub-viral agents  Classical example; Endings for taxa of viroids are:  Word viroid for species  Suffix -viroid for genera  -viroinae for sub-families and  -viroidae for families  ?
  • 82. Classification of Subviral agents  1. FAMILY DELTAVIRIDAE  2. SLOW VIRUSES
  • 83. 1. FAMILY DELTAVIRIDAE -One Genus: Deltavirus -Contains Hepatitis D virus a.k.a Delta agent -A defective RNA virus, replicates in HBV infected hepatocytes
  • 84. 2. SLOW VIRUSES -Prions, Proteinacious infectious or prion protein (Prp) agent referred to as unconventional viruses -Cause group of Diseases called Prion Diseases known as Transmissible Spongiform Encephalopathy (TSE) a. Human (Kuru, Cannibalism; 1957; 1st among fore tribe in eastern island of Papua New Guinea) Creutzfeldt- Jakob Disease; Gerstmann- Straussler Scheinker (GSS) Disease; Fatal familial insomnia(FFI) b. Animal (Scrapie, Mad Cow Dis, Bovine Spongiform Encephalopathy)
  • 85. Thank you all.
  • 86. FURTHER READING  Anjorin, A. A., Omilabu, S. A., Salu, O. B., Oke, B. O. (2012). Detection of Influenza A virus in Pigs in Lagos, Nigeria. Afr. J. Cln. Exper. Microbiol, 13(1): 41-45. http://dx.doi.org/10.4314/ajcem/v13i1  Brooks, GF, Carol, KC, Butel, JS, Morse, SA. (2007). Selected Medically Important Microorganisms. Viruses. In: Jawetz, Melnick and Adelberg’s Medical Microbiology. Mc Graw Hill, New York.  Cheesbrough M. (2002). District Laboratory Practice in Tropical Countries Part 2. Cambridge University Press, UK  El-Azizi, M. Lecture 1 General virology.  Fagbami AH (2008). Medical Virology Lecture Supplements. Nihinco Prints Mokola, Ibadan.  Knipe, D. M. and Howley, P. M. (2007). Fields Virology. Vol. 1. 5th Edition. Lippincott Williams & Wilkins
  • 87.  Lodish H, Berk A, Zipursky SL, et al., (2000). Molecular Cell Biology. 4th edition. Freeman and Company, New York:  Mahy, B.W.J. (2009). The Dictionary of Virology. Fourth Edition. Academic Press, UK  Oyefolu, A. O. B. (2008). Unpublished Virology Lecture Series. Department of Microbiology, LASU, Lagos.  Obayori, O. S. (2008). Unpublished Virology Lecture Series. Department of Microbiology, LASU, Lagos.  Sander, D. (2007). The Big Picture Book of Viruses. http://www.virology.net/big_virology/BVFamilyGenome.html  Wikipedia (2012). ICTV. http://en.wikipedia.org/wiki/International_Committee_on_Taxonom y_of_Viruses